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FFPE ChIP-Seq

obtain ChIP-Seq data from clinical samples

Epigenetic misregulation is now known to contribute to diseases such as cancer. In cancer, mutations in the enzymes that regulate histone modification deposition and removal are mutated at a high frequency and these mutations result in alterations in global histone modification patterns. Understanding changes in global histone modification landscapes can provide clues to cellular origins, disease progression and possibly, patient outcome. In order to fully realize the potential of global histone modification profiling toward advances in disease biology and clinical outcomes, it will be necessary to generate profiles using FFPE preserved patient samples. However, ChIP-Seq, the technique that is used to generate these profiles, is challenging and has traditionally required cell numbers that are much greater than what can be obtained from FFPE sections. To address this limitation, scientists at Active Motif have developed the ability to perform ChIP-Seq from limited amounts of formalin-fixed, paraffin-embedded (FFPE) tissue.

The FFPE ChIP-Seq Service Includes:

  • Chromatin isolation from FFPE blocks, slides or sections*.
  • Immunoprecipitation using a robust histone modification or TF antibody.
  • Library construction for Next-Gen sequencing.
  • Next-Gen sequencing using an Illumina sequencer.
  • Data Analysis.

*Active Motif will recommend the amount of material to be supplied, which will depend on the tissue type being used. Typically > 5 sections (10µm) per ChIP-Seq experiment are necessary.

To learn more, please give us a call or send us an Epigenetic Services Information Request. You can also download Active Motif’s Epigenetic Services Profile.

 
Name Cat No. Price  
FFPE ChIP-Seq 25019 Request Quote
Sequencing of Input / Control DNA 25046 Request Quote

FFPE ChIP-Seq Data

Active Motif has performed FFPE ChIP-Seq from clinical samples that have been preserved for more than 10 years. Sample types include tumor and matched normal tissue from human liver, kidney, colon and others. These assays have been performed successfully using robust ChIP-Seq validated antibodies against histone modifications.

ChIP-Seq performed using antibodies against H3K4me3 and H3K36me3
Figure 1: FFPE ChIP-Seq performed using 20 year old colon tumor FFPE block and antibodies against H3K4me3 and H3K36me3.

Chromatin was extracted from 5 x 10 µm sections derived from a 20 year old colon tumor FFPE block and ChIP-Seq was performed using antibodies against H3K4me3 and H3K36me3. Each ChIP reaction used approximately 1/3rd of the chromatin preparation. Roughly 500,000 bases of the human genome are depicted in the image above showing H3K4me3 occupancy at promoters and H3K36me3 occupancy across gene bodies.

ChIP-Seq performed using antibodies against H3K27ac and H3K27me3
Figure 2: FFPE ChIP-Seq performed using 20 year old colon tumor FFPE block and antibodies against H3K27ac and H3K27me3.

Chromatin was extracted from 5 x 10 µm sections derived from a 20 year old colon tumor FFPE block and ChIP-Seq was performed using antibodies against H3K27ac and H3K27me3. Each ChIP reaction used only 1/3rd of the chromatin preparation. Roughly 2.4 million bases of the human genome are depicted in the image above showing mutually exclusive binding of the enhancer mark H3K27ac and the repressive mark, H3K27me3.

ChIP-Seq performed using antibodies against H3K27ac and H3K27me3
Figure 3: FFPE ChIP-Seq performed using 2 human Glioblastoma biopsies and an antibody against H3K27ac.

Biopsies were provided as both FFPE prepared samples (blue) and fresh/frozen samples (green). FFPE and fresh/frozen ChIP-Seq data sets were similar. Tumor-specific H3K27ac occupancy was detectable in the FFPE and fresh/frozen data sets (highlighted in red).

ChIP-Seq performed using antibodies against H3K27ac and H3K27me3
Figure 4: FFPE ChIP-Seq performed using 2 human Glioblastoma biopsies and an antibody against H3K27ac.

Biopsies were provided as both FFPE prepared samples (blue) and fresh/frozen samples (green). FFPE and fresh/frozen ChIP-Seq data sets were similar. Tumor-specific H3K27ac occupancy was detectable in the FFPE and fresh/frozen data sets (highlighted in red).

ChIP-Seq performed using antibodies against H3K27ac and H3K27me3
Figure 5: FFPE ChIP-Seq performed using 2 human Glioblastoma biopsies and an antibody against H3K27ac.

Biopsies were provided as both FFPE prepared samples (blue) and fresh/frozen samples (green). FFPE and fresh/frozen ChIP-Seq data sets were similar. Tumor-specific H3K27ac occupancy was detectable in the FFPE and fresh/frozen data sets (highlighted in red).

ChIP-Seq performed using antibodies against H3K27ac and H3K27me3
Figure 6: FFPE ChIP-Seq was performed using chromatin from two human tumor biopsies and an antibody against H3K27ac.

The highlighted region shows a differential Super Enhancer.

FFPE ChIP-Seq performed using a human Glioblastoma biopsy and an antibody against H3K27me3
Figure 7: FFPE ChIP-Seq performed using a human Glioblastoma biopsy and an antibody against H3K27me3.

The biopsy was provided as both a fresh/frozen samples and FFPE tissue block. FFPE and fresh/frozen ChIP-Seq data sets gave similar results. The image shows a typical H3K27me3 occupancy pattern of long stretches of the genome being marked by H3K27me3.

FFPE ChIP-Seq performed using a human Glioblastoma biopsy and an antibody against H3K27me3
Figure 8: FFPE ChIP-Seq performed using a human Glioblastoma biopsy and an antibody against H3K27me3.

The biopsy was provided as both a fresh/frozen samples and FFPE tissue block. FFPE and fresh/frozen ChIP-Seq data sets gave similar results. The image shows a typical H3K27me3 occupancy pattern of long stretches of the genome being marked by H3K27me3.